The DBCLS BioHackathon

Standardization and interoperability for bioinformatics web services and workflows

Toshiaki Katayama, Kazuharu Arakawa, Mitsuteru Nakao, Keiichiro Ono, Kiyoko F. Aoki-Kinoshita, Yasunori Yamamoto, Atsuko Yamaguchi, Shuichi Kawashima, Hong Woo Chun, Jan Aerts, Bruno Aranda, Lord H. Barboza, Raoul J P Bonnal, Richard Bruskiewich, Jan C. Bryne, José M. Fernández, Akira Funahashi, Paul M K Gordon, Naohisa Goto, Andreas Groscurth & 37 others Alex Gutteridge, Richard Holland, Yoshinobu Kano, Edward A. Kawas, Arnaud Kerhornou, Eri Kibukawa, Akira R. Kinjo, Michael Kuhn, Hilmar Lapp, Heikki Lehvaslaiho, Hiroyuki Nakamura, Yasukazu Nakamura, Tatsuya Nishizawa, Chikashi Nobata, Tamotsu Noguchi, Thomas M. Oinn, Shinobu Okamoto, Stuart Owen, Evangelos Pafilis, Matthew Pocock, Pjotr Prins, René Ranzinger, Florian Reisinger, Lukasz Salwinski, Mark Schreiber, Martin Senger, Yasumasa Shigemoto, Daron M. Standley, Hideaki Sugawara, Toshiyuki Tashiro, Oswaldo Trelles, Rutger A. Vos, Mark D. Wilkinson, William York, Christian M. Zmasek, Kiyoshi Asai, Toshihisa Takagi

Research output: Contribution to journalArticle

18 Citations (Scopus)

Abstract

Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient systems without the need to transfer entire databases for every step of an analysis. However, various incompatibilities among database resources and analysis services make it difficult to connect and integrate these into interoperable workflows. To resolve this situation, we invited domain specialists from web service providers, client software developers, Open Bio* projects, the BioMoby project and researchers of emerging areas where a standard exchange data format is not well established, for an intensive collaboration entitled the BioHackathon 2008. The meeting was hosted by the Database Center for Life Science (DBCLS) and Computational Biology Research Center (CBRC) and was held in Tokyo from February 11th to 15th, 2008. In this report we highlight the work accomplished and the common issues arisen from this event, including the standardization of data exchange formats and services in the emerging fields of glycoinformatics, biological interaction networks, text mining, and phyloinformatics. In addition, common shared object development based on BioSQL, as well as technical challenges in large data management, asynchronous services, and security are discussed. Consequently, we improved interoperability of web services in several fields, however, further cooperation among major database centers and continued collaborative efforts between service providers and software developers are still necessary for an effective advance in bioinformatics web service technologies.

Original languageEnglish
Article number8
JournalJournal of Biomedical Semantics
Volume1
DOIs
Publication statusPublished - 2010 Aug 21
Externally publishedYes

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Workflow
Biological Science Disciplines
Bioinformatics
Computational Biology
Interoperability
Web services
Standardization
Databases
Electronic data interchange
Software
Technology
Data Mining
Tokyo
Information management
Research Personnel
Research

ASJC Scopus subject areas

  • Information Systems
  • Computer Science Applications
  • Computer Networks and Communications
  • Health Informatics

Cite this

The DBCLS BioHackathon : Standardization and interoperability for bioinformatics web services and workflows. / Katayama, Toshiaki; Arakawa, Kazuharu; Nakao, Mitsuteru; Ono, Keiichiro; Aoki-Kinoshita, Kiyoko F.; Yamamoto, Yasunori; Yamaguchi, Atsuko; Kawashima, Shuichi; Chun, Hong Woo; Aerts, Jan; Aranda, Bruno; Barboza, Lord H.; Bonnal, Raoul J P; Bruskiewich, Richard; Bryne, Jan C.; Fernández, José M.; Funahashi, Akira; Gordon, Paul M K; Goto, Naohisa; Groscurth, Andreas; Gutteridge, Alex; Holland, Richard; Kano, Yoshinobu; Kawas, Edward A.; Kerhornou, Arnaud; Kibukawa, Eri; Kinjo, Akira R.; Kuhn, Michael; Lapp, Hilmar; Lehvaslaiho, Heikki; Nakamura, Hiroyuki; Nakamura, Yasukazu; Nishizawa, Tatsuya; Nobata, Chikashi; Noguchi, Tamotsu; Oinn, Thomas M.; Okamoto, Shinobu; Owen, Stuart; Pafilis, Evangelos; Pocock, Matthew; Prins, Pjotr; Ranzinger, René; Reisinger, Florian; Salwinski, Lukasz; Schreiber, Mark; Senger, Martin; Shigemoto, Yasumasa; Standley, Daron M.; Sugawara, Hideaki; Tashiro, Toshiyuki; Trelles, Oswaldo; Vos, Rutger A.; Wilkinson, Mark D.; York, William; Zmasek, Christian M.; Asai, Kiyoshi; Takagi, Toshihisa.

In: Journal of Biomedical Semantics, Vol. 1, 8, 21.08.2010.

Research output: Contribution to journalArticle

Katayama, T, Arakawa, K, Nakao, M, Ono, K, Aoki-Kinoshita, KF, Yamamoto, Y, Yamaguchi, A, Kawashima, S, Chun, HW, Aerts, J, Aranda, B, Barboza, LH, Bonnal, RJP, Bruskiewich, R, Bryne, JC, Fernández, JM, Funahashi, A, Gordon, PMK, Goto, N, Groscurth, A, Gutteridge, A, Holland, R, Kano, Y, Kawas, EA, Kerhornou, A, Kibukawa, E, Kinjo, AR, Kuhn, M, Lapp, H, Lehvaslaiho, H, Nakamura, H, Nakamura, Y, Nishizawa, T, Nobata, C, Noguchi, T, Oinn, TM, Okamoto, S, Owen, S, Pafilis, E, Pocock, M, Prins, P, Ranzinger, R, Reisinger, F, Salwinski, L, Schreiber, M, Senger, M, Shigemoto, Y, Standley, DM, Sugawara, H, Tashiro, T, Trelles, O, Vos, RA, Wilkinson, MD, York, W, Zmasek, CM, Asai, K & Takagi, T 2010, 'The DBCLS BioHackathon: Standardization and interoperability for bioinformatics web services and workflows', Journal of Biomedical Semantics, vol. 1, 8. https://doi.org/10.1186/2041-1480-1-8
Katayama, Toshiaki ; Arakawa, Kazuharu ; Nakao, Mitsuteru ; Ono, Keiichiro ; Aoki-Kinoshita, Kiyoko F. ; Yamamoto, Yasunori ; Yamaguchi, Atsuko ; Kawashima, Shuichi ; Chun, Hong Woo ; Aerts, Jan ; Aranda, Bruno ; Barboza, Lord H. ; Bonnal, Raoul J P ; Bruskiewich, Richard ; Bryne, Jan C. ; Fernández, José M. ; Funahashi, Akira ; Gordon, Paul M K ; Goto, Naohisa ; Groscurth, Andreas ; Gutteridge, Alex ; Holland, Richard ; Kano, Yoshinobu ; Kawas, Edward A. ; Kerhornou, Arnaud ; Kibukawa, Eri ; Kinjo, Akira R. ; Kuhn, Michael ; Lapp, Hilmar ; Lehvaslaiho, Heikki ; Nakamura, Hiroyuki ; Nakamura, Yasukazu ; Nishizawa, Tatsuya ; Nobata, Chikashi ; Noguchi, Tamotsu ; Oinn, Thomas M. ; Okamoto, Shinobu ; Owen, Stuart ; Pafilis, Evangelos ; Pocock, Matthew ; Prins, Pjotr ; Ranzinger, René ; Reisinger, Florian ; Salwinski, Lukasz ; Schreiber, Mark ; Senger, Martin ; Shigemoto, Yasumasa ; Standley, Daron M. ; Sugawara, Hideaki ; Tashiro, Toshiyuki ; Trelles, Oswaldo ; Vos, Rutger A. ; Wilkinson, Mark D. ; York, William ; Zmasek, Christian M. ; Asai, Kiyoshi ; Takagi, Toshihisa. / The DBCLS BioHackathon : Standardization and interoperability for bioinformatics web services and workflows. In: Journal of Biomedical Semantics. 2010 ; Vol. 1.
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abstract = "Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient systems without the need to transfer entire databases for every step of an analysis. However, various incompatibilities among database resources and analysis services make it difficult to connect and integrate these into interoperable workflows. To resolve this situation, we invited domain specialists from web service providers, client software developers, Open Bio* projects, the BioMoby project and researchers of emerging areas where a standard exchange data format is not well established, for an intensive collaboration entitled the BioHackathon 2008. The meeting was hosted by the Database Center for Life Science (DBCLS) and Computational Biology Research Center (CBRC) and was held in Tokyo from February 11th to 15th, 2008. In this report we highlight the work accomplished and the common issues arisen from this event, including the standardization of data exchange formats and services in the emerging fields of glycoinformatics, biological interaction networks, text mining, and phyloinformatics. In addition, common shared object development based on BioSQL, as well as technical challenges in large data management, asynchronous services, and security are discussed. Consequently, we improved interoperability of web services in several fields, however, further cooperation among major database centers and continued collaborative efforts between service providers and software developers are still necessary for an effective advance in bioinformatics web service technologies.",
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T2 - Standardization and interoperability for bioinformatics web services and workflows

AU - Katayama, Toshiaki

AU - Arakawa, Kazuharu

AU - Nakao, Mitsuteru

AU - Ono, Keiichiro

AU - Aoki-Kinoshita, Kiyoko F.

AU - Yamamoto, Yasunori

AU - Yamaguchi, Atsuko

AU - Kawashima, Shuichi

AU - Chun, Hong Woo

AU - Aerts, Jan

AU - Aranda, Bruno

AU - Barboza, Lord H.

AU - Bonnal, Raoul J P

AU - Bruskiewich, Richard

AU - Bryne, Jan C.

AU - Fernández, José M.

AU - Funahashi, Akira

AU - Gordon, Paul M K

AU - Goto, Naohisa

AU - Groscurth, Andreas

AU - Gutteridge, Alex

AU - Holland, Richard

AU - Kano, Yoshinobu

AU - Kawas, Edward A.

AU - Kerhornou, Arnaud

AU - Kibukawa, Eri

AU - Kinjo, Akira R.

AU - Kuhn, Michael

AU - Lapp, Hilmar

AU - Lehvaslaiho, Heikki

AU - Nakamura, Hiroyuki

AU - Nakamura, Yasukazu

AU - Nishizawa, Tatsuya

AU - Nobata, Chikashi

AU - Noguchi, Tamotsu

AU - Oinn, Thomas M.

AU - Okamoto, Shinobu

AU - Owen, Stuart

AU - Pafilis, Evangelos

AU - Pocock, Matthew

AU - Prins, Pjotr

AU - Ranzinger, René

AU - Reisinger, Florian

AU - Salwinski, Lukasz

AU - Schreiber, Mark

AU - Senger, Martin

AU - Shigemoto, Yasumasa

AU - Standley, Daron M.

AU - Sugawara, Hideaki

AU - Tashiro, Toshiyuki

AU - Trelles, Oswaldo

AU - Vos, Rutger A.

AU - Wilkinson, Mark D.

AU - York, William

AU - Zmasek, Christian M.

AU - Asai, Kiyoshi

AU - Takagi, Toshihisa

PY - 2010/8/21

Y1 - 2010/8/21

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